R help - Oct 2007 - Rooting trees using ape

Hi all,

I seem to be having a difficult time using the 'ape' package in R  
when it comes to rooting trees.  Here's a short screenshot:

 > nirK.tree

Phylogenetic tree with 23 tips and 21 internal nodes.

Tip labels:
	Burkholder, Burkholde3, Burkholde1, Burkholde4, Burkholde5,  
Ralstonia2, ...
	Node labels:
	, 100, 100, 100, 70, 91,...

Unooted; includes branch lengths.
 > test<-root(nirk.tree, 4)
Error in root(nirk.tree, 4) : subscript out of bounds
 > test<-root(nirk.tree, "Burkholde4")
Error in root(nirk.tree, "Burkholde4") : subscript out of bounds
 >

I tried with the example tree provided in the package, and that  
seemed to work ok.  Any suggestions?

Many thanks,
Chris

Chris Jones-35 wrote:
> 
> Hi all,
> 
> I seem to be having a difficult time using the 'ape' package in R  
> when it comes to rooting trees.  Here's a short screenshot:
> 
> [snip]
> 
> 
  Can you post your dataset, or a subset of it that replicates
the problem, somewhere?  (On the list if short, otherwise
on some web site somewhere.)   [See "reproducible
example" in the posting guide.]

  cheers
    Ben Bolker

-- 
View this message in context:
http://www.nabble.com/Rooting-trees-using-ape-tf4600839.html#a13140596
Sent from the R help mailing list archive at Nabble.com.

Please supply enough information to allow us to reproduce the error.
Also, nirK.tree is a different object to nirk.tree, which might be
confusing things.

Simon.

On Wed, 2007-10-10 at 15:07 +0200, Chris Jones wrote:
> Hi all,
> 
> I seem to be having a difficult time using the 'ape' package in R  
> when it comes to rooting trees.  Here's a short screenshot:
> 
>  > nirK.tree
> 
> Phylogenetic tree with 23 tips and 21 internal nodes.
> 
> Tip labels:
> 	Burkholder, Burkholde3, Burkholde1, Burkholde4, Burkholde5,  
> Ralstonia2, ...
> 	Node labels:
> 	, 100, 100, 100, 70, 91,...
> 
> Unooted; includes branch lengths.
>  > test<-root(nirk.tree, 4)
> Error in root(nirk.tree, 4) : subscript out of bounds
>  > test<-root(nirk.tree, "Burkholde4")
> Error in root(nirk.tree, "Burkholde4") : subscript out of bounds
>  >
> 
> I tried with the example tree provided in the package, and that  
> seemed to work ok.  Any suggestions?
> 
> Many thanks,
> Chris
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
Simon Blomberg, BSc (Hons), PhD, MAppStat. 
Lecturer and Consultant Statistician 
Faculty of Biological and Chemical Sciences 
The University of Queensland 
St. Lucia Queensland 4072 
Australia
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T: +61 7 3365 2506 
email: S.Blomberg1_at_uq.edu.au

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